BuildFromScratch

Singularity build from Sandbox

The following tutorial will involve the creation of a container for the STAR (RNA-Seq) aligner.

# Creating Container from Scratch
sudo singularity build --sandbox STARSingularity/ docker://ubuntu

# Begin Modifying Container
sudo singularity shell --writable STARSingularity/

Important Notes:

• Using sandbox parameters creates folder system instead of single file so we can modify the container.

• To make any permant changes to container we must use the singularity shell --writeable command.

# Once inside container shell environment. Install necessary dependencies:

# Always do this first
apt update

# Install dependencies.
apt install libbz2-dev
apt install liblzma-dev
apt install zlib1g-dev
apt-get install g++
apt install wget
apt install unzip
apt install nano

wget https://github.com/alexdobin/STAR/releases/download/2.7.11a/STAR_2.7.11a.zip
unzip STAR_2.7.11a.zip


# Move STAR Binary to sbin folder.
mv ./STAR_2.7.11a/Linux_x86_64/STAR /usr/local/sbin/

Now exit out of singularity using (CMD+D). We can now test if STAR can be executed from outside the container.

# Confirm container works: 
singularity exec STARSingularity STAR --help

---

Convert to Production container (SIF) file

Once we have finished building a container environment in sandbox mode it is best pratice to release a production version.

sudo singularity build STARSingularityProduction.sif STARSingularity

To confirm the production container works we can run:

singularity exec STARSingularityProduction.sif STAR --help

---

Adding Runscript

When building a container there may be certain commands which you want to run as soon as the contain is called via the command:

singularity run STARSingularity 

This is alternative to using singularity exec command where you have to parse the command.

When building a container from scratch the way to create the runscript is to modify a file called 'singularity' as shown below:

sudo singularity shell --writable STARSingularity/

nano /singularity

Then delete what is in the file which is automatically added when creating the sandbox container and replace it with:

#!/bin/sh

echo "Positional Arguments:"
for arg in "$@"; do
    echo "$arg"
done

This run script will parse commands given to it and print these as positional arguments. To validate this:

singularity run STARSingularity My First Container

The output should be:

Positional Arguments:
My
First
Container

By modicfying the run script we can standardise container inputs and outputs.